The history of BONUS dates back to the year 2003, when BONUS ERA-NET started. At that time, there was no large-scale cooperation between Baltic Sea research funding organisations, only two- or three-lateral cooperation activities between different countries. ERA-NET instrument of the EU´s 6th Framework Programme was considered as an appropriate tool to develop and broaden the Baltic Sea research funding cooperation.

During the lifetime on BONUS ERA-NET, several activities have been implemented, including writing of the BONUS-169 Science Plan and launching the first joint BONUS+ Call. More detailed information on BONUS ERA-NET activities can be found at BONUS ERA-NET Work packages and in BONUS Publication series.

In the year 2005, BONUS ERA-NET was invited to Article-169 negotiations along with some other initiatives. In 2006, the European Commission decided that BONUS would proceed to Article-169 phase in 2008/2009.

In order to the Article-169 to be implemented, a dedicated legal structure was demanded. BONUS Baltic Organisations Network for Funding Science EEIG, BONUS EEIG in short, was established for this purpose in the spring 2007.

The Secretariat of BONUS EEIG was established in Helsinki and in addition to running the everyday administration of BONUS EEIG, the Secretariat also takes care of the coordination of BONUS ERA-NET and management of the BONUS-169 Joint Baltic Sea Research Programme.